TABLE 1.

Data set descriptions and summary results

Data set	MAF classa	Populationsb	Individuals	Loci	%c	CC%d	CT%e	CT%, single locusf	g	% rare and commonh	% fixed and commoni	j	% het.k
Insertions	All	Distinct (3)	219	175	10	0.46	0	56	14	21	10	18	32
Insertions	Rare	Distinct (3)	219	21	47	58	39	66	12	57	33	5.7	7.0
Insertions	Common	Distinct (3)	219	154	9.1	0.46	0	55	14	16	7.1	20	36
Insertions	All	All (4)	259	175	15	3.1	1.2	65	12	23	11	15	32
Insertions	Rare	All (4)	259	21	50	76	46	73	8.3	62	43	4.3	7.5
Insertions	Common	All (4)	259	154	13	3.1	0.77	64	12	18	6.5	17	36
Microarray	All	Distinct (3)	137	9,922	0	0	0	56	15	26	12	20	32
Microarray	Rare	Distinct (3)	137	920	17	7.3	0	65	10	87	56	9.5	10
Microarray	Common	Distinct (3)	137	9,002	0	0	0	55	15	19	7.8	21	34
Microarray	All	All (8)	278	9,922	3.1	10	1.1	82	13	44	27	18	32
Microarray	Rare	All (8)	278	851	36	72	1.4	84	8.9	98	88	7.9	11
Microarray	Common	All (8)	278	9,071	3.3	8.3	1.1	81	13	39	21	19	34
Resequenced	All	All (3)	209	14,233	8.2	0	0	57	13	40	29	11	17
Resequenced	Rare	All (3)	209	8,389	29	45	0.96	59	9.6	51	43	4.6	4.7
Resequenced	Common	All (3)	209	5,844	5.9	0.96	0	53	14	23	8.4	19	34

^aSets of loci with MAF < 0.1 (rare), MAF > 0.1 (common), or any MAF (all).

^bSets of individuals representing all populations in a data set or only the more distinct populations.

^cDissimilarity fraction.

^dCentroid misclassification rate.

^ePopulation trait value misclassification rate.

^fTrait value misclassification rate based on a single locus, averaged over all loci.

^gThe proportion of variance in allelic frequencies attributable to population differences.

^hPercentage of loci with MAF < 0.1 in one population and MAF > 0.1 in another.

ⁱPercentage of loci that are monomorphic in one population and polymorphic with MAF > 0.1 in another.

^jAverage difference in allele frequency between populations, averaged across alleles, loci, and population pairs.

^kPercentage of individuals heterozygous at each locus, averaged across all loci.